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JBrowse Configuration Guide

Tue, 03/24/2020 - 16:46

← Older revision Revision as of 20:46, 24 March 2020 Line 3,492: Line 3,492:         //page.on('console', msg => console.log('PAGE LOG:', msg.text()));        //page.on('console', msg => console.log('PAGE LOG:', msg.text()));         await page.setViewport({        await page.setViewport({ −         width:argv[4]||1000,+         width:+argv[4]||1000, −         height:argv[5]||600,+         height:+argv[5]||600,           deviceScaleFactor:argv[6]||2          deviceScaleFactor:argv[6]||2         });        }); Colin Diesh
Categories: Bio

GSOC Project Ideas 2020

Wed, 03/18/2020 - 22:14

‎Community access portal to Reactome Archive (Reactome)

← Older revision Revision as of 02:14, 19 March 2020 (2 intermediate revisions by the same user not shown)Line 98: Line 98:  * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca) * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca)    −==Creating NCBI GeneRIFs and other data exports (Reactome)==+==Community access portal to Reactome Archive (Reactome)== −**''Brief explanation:'' Reactome already links to NCBI Gene, Protein, and OMIM web pages. NCBI has a mechanism that third party collaborators can use to add information to RefSeq and NCBI Gene using the GeneRIF system. We will create an export tool to contribute summary sentences detailing pathways, reactions and complexes that the gene participates in, including the gene’s functional role, with PubMed and Reactome stable identifiers that will allow linkage back to the relevant Reactome pathway and curated literature. Other data exports are under consideration.+*''Brief explanation:'' Reactome generates new pathway and other annotation data on a quarterly basis. With each new release, the preceding data set is archived to an AWS S3 bucket. As part of our data sharing policy, we would like to develop web interface to allow users to request specific versions of archived data and to make it available to download.   −**''Expected results:'' Scripts to export data, QA steps, export data files.+*''Expected results:'' Web interface for users to request data and download via a shareable link that either expires within a certain timeframe or after data is downloaded.  * ''Project Home Page URL:'' [https://reactome.org. reactome.org]. * ''Project Home Page URL:'' [https://reactome.org. reactome.org]. −* ''Knowledge prerequisites:'' Java, MySQL and/or Neo4j+* ''Knowledge prerequisites:'' Java, AWS, Joomla  * ''Skill level:'' Medium. * ''Skill level:'' Medium.  * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca) * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca) −  −Community access portal to Reactome Archive.  −      == Community data submission (WormBase) == == Community data submission (WormBase) == Robin.haw
Categories: Bio

GSOC Project Ideas 2020

Wed, 03/18/2020 - 22:14

‎Community access portal to Reactome Archive (Reactome)

← Older revision Revision as of 02:14, 19 March 2020 (5 intermediate revisions by the same user not shown)Line 71: Line 71:  * ''Knowledge prerequisites:''  Java, MySQL, (optional) Neo4j, AWS * ''Knowledge prerequisites:''  Java, MySQL, (optional) Neo4j, AWS  * ''Skill level:'' Medium * ''Skill level:'' Medium −* ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca)+* ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca) and Robin Haw (robin.haw[AT]oicr.on.ca)     == GraphDB API (Reactome) == == GraphDB API (Reactome) == Line 80: Line 80:  * ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary. * ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary.  * ''Skill level:'' Advanced. * ''Skill level:'' Advanced. −* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca).+* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca)     == GraphQL interface for querying Reactome data (Reactome) == == GraphQL interface for querying Reactome data (Reactome) == Line 95: Line 95:  * ''Project Home Page URL:'' [https://reactome.org. reactome.org]. * ''Project Home Page URL:'' [https://reactome.org. reactome.org].  * ''Knowledge prerequisites:'' Java, MySQL and/or Neo4j, creating visuals for statistical data (preferred but not required) * ''Knowledge prerequisites:'' Java, MySQL and/or Neo4j, creating visuals for statistical data (preferred but not required)  +* ''Skill level:'' Medium.  +* ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca)  +  +==Community access portal to Reactome Archive (Reactome)==  +*''Brief explanation:'' Reactome generates new pathway and other annotation data on a quarterly basis. With each new release, the preceding data set is archived to an AWS S3 bucket. As part of our data sharing policy, we would like to develop web interface to allow users to request specific versions of archived data and to make it available to download.   +*''Expected results:'' Web interface for users to request data and download via a shareable link that either expires within a certain timeframe or after data is downloaded.  +* ''Project Home Page URL:'' [https://reactome.org. reactome.org].  +* ''Knowledge prerequisites:'' Java, AWS, Joomla  * ''Skill level:'' Medium. * ''Skill level:'' Medium.  * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca) * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca) Robin.haw
Categories: Bio

GSOC Project Ideas 2020

Wed, 03/18/2020 - 09:46

‎Proposed project ideas for 2020

← Older revision Revision as of 13:46, 18 March 2020 (2 intermediate revisions by the same user not shown)Line 71: Line 71:  * ''Knowledge prerequisites:''  Java, MySQL, (optional) Neo4j, AWS * ''Knowledge prerequisites:''  Java, MySQL, (optional) Neo4j, AWS  * ''Skill level:'' Medium * ''Skill level:'' Medium −* ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca)+* ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca) and Robin Haw (robin.haw[AT]oicr.on.ca)     == GraphDB API (Reactome) == == GraphDB API (Reactome) == Line 80: Line 80:  * ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary. * ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary.  * ''Skill level:'' Advanced. * ''Skill level:'' Advanced. −* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca).+* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca)     == GraphQL interface for querying Reactome data (Reactome) == == GraphQL interface for querying Reactome data (Reactome) == Line 97: Line 97:  * ''Skill level:'' Medium. * ''Skill level:'' Medium.  * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca) * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca)  +  +==Creating NCBI GeneRIFs and other data exports (Reactome)==  +**''Brief explanation:'' Reactome already links to NCBI Gene, Protein, and OMIM web pages. NCBI has a mechanism that third party collaborators can use to add information to RefSeq and NCBI Gene using the GeneRIF system. We will create an export tool to contribute summary sentences detailing pathways, reactions and complexes that the gene participates in, including the gene’s functional role, with PubMed and Reactome stable identifiers that will allow linkage back to the relevant Reactome pathway and curated literature. Other data exports are under consideration.  +**''Expected results:'' Scripts to export data, QA steps, export data files.  +* ''Project Home Page URL:'' [https://reactome.org. reactome.org].  +* ''Knowledge prerequisites:'' Java, MySQL and/or Neo4j  +* ''Skill level:'' Medium.  +* ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca)  +  +Community access portal to Reactome Archive.  +     == Community data submission (WormBase) == == Community data submission (WormBase) == Robin.haw
Categories: Bio

GSOC Project Ideas 2020

Mon, 03/16/2020 - 21:56

‎JBrowse 2 - Phylogenetic tree viewer

← Older revision Revision as of 01:56, 17 March 2020 (2 intermediate revisions by the same user not shown)Line 156: Line 156:  * ''Expected results:'' A beautiful and fast tree viewer in JBrowse 2, written using React and mobx-state-tree. * ''Expected results:'' A beautiful and fast tree viewer in JBrowse 2, written using React and mobx-state-tree.  * ''Project Home Page URL:'' https://jbrowse.org   * ''Project Home Page URL:'' https://jbrowse.org    +* ''Project Chat:'' https://gitter.im/GMOD/jbrowse  * ''Knowledge prerequisites:'' JavaScript, React * ''Knowledge prerequisites:'' JavaScript, React  * ''Skill level:'' Advanced * ''Skill level:'' Advanced Line 164: Line 165:  * ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects * ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects  * ''Project Home Page URL:'' https://jbrowse.org   * ''Project Home Page URL:'' https://jbrowse.org    +* ''Project Chat:'' https://gitter.im/GMOD/jbrowse  * ''Knowledge prerequisites:'' JavaScript, React * ''Knowledge prerequisites:'' JavaScript, React  * ''Skill level:'' Medium * ''Skill level:'' Medium Line 172: Line 174:  * ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects * ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects  * ''Project Home Page URL:'' https://jbrowse.org   * ''Project Home Page URL:'' https://jbrowse.org    +* ''Project Chat:'' https://gitter.im/GMOD/jbrowse  * ''Knowledge prerequisites:'' JavaScript, React * ''Knowledge prerequisites:'' JavaScript, React  * ''Skill level:'' Advanced * ''Skill level:'' Advanced  * ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie) * ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie) Colin Diesh
Categories: Bio

GSOC Project Ideas 2020

Fri, 03/13/2020 - 18:49

‎Automated Bioinformatics Help in Galaxy: Added mentors

← Older revision Revision as of 22:49, 13 March 2020 Line 40: Line 40:  * ''Knowledge prerequisites:''  programming language(s) to be used, plus any other particular computer science skills needed. * ''Knowledge prerequisites:''  programming language(s) to be used, plus any other particular computer science skills needed.  * ''Skill level:'' Medium. * ''Skill level:'' Medium. −* ''Mentors:''+* ''Mentors:'' [https://galaxyproject.org/people/sergey/ Sergey Golitsynskiy], [[User:Clements|Dave Clements]]     == Use Galaxy to run Reactome analysis and processes on genomic data (Reactome) == == Use Galaxy to run Reactome analysis and processes on genomic data (Reactome) == Clements
Categories: Bio

User:Jmill3082

Thu, 03/12/2020 - 20:06

Creating user page for new user.

New page

Graduate student at Johns Hopkins University.
NSF Graduate Research Fellow.
Working in the Gordus lab in the Biology Department.
I am interested in how behaviors that are structured over long timescales are coded genetically and at the cellular/circuit level in the brain.
I am using the orb-weaving spider Uloborus diversus to study the web-building behavior.
Currently, I am working on annotating the genome of this organism. Scott
Categories: Bio

User:Jmill3082

Thu, 03/12/2020 - 20:06

User account Jmill3082 was created by Scott

Scott
Categories: Bio

User:Garrett

Thu, 03/12/2020 - 19:45

Creating user page for new user.

New page

Garrett has been a core developer for JBrowse since 2018, working for Ian Holmes at UC Berkeley. He graduated from the University of Utah with a BS in Physics in 2015 and Brandeis University with an MS in Bioinformatics in 2019. He currently lives near Salt Lake City, UT, but has also lived in Massachusetts and Japan. Scott
Categories: Bio

User:Garrett

Thu, 03/12/2020 - 19:45

User account Garrett was created by Scott

Scott
Categories: Bio

GSOC Project Ideas 2020

Wed, 03/11/2020 - 15:45

‎Statistics consolidation/display of release data (Reactome)

← Older revision Revision as of 19:45, 11 March 2020 Line 90: Line 90:  * ''Mentors:'' Joel Weiser (joel.weiser[AT]oicr.on.ca) * ''Mentors:'' Joel Weiser (joel.weiser[AT]oicr.on.ca)    −== Statistics consolidation/display of release data (Reactome) ==+== Centralized dashboard or metrics system (Reactome) == −* ''Brief explanation:'' Reactome has both manual and automated statistical tracking of its quarterly release data.  This project would seek to fully automate and consolidate the quantification of release data measurement for metrics such as the number of pathways, reactions, distinct proteins (with and without UniProt isoforms), complexes, small molecules, drugs/therapeutics, literature references, etc. for human (curated) and non-human (electronically inferred) species and stratified for normal and disease biology+* ''Brief explanation:'' Reactome has both manual and automated statistical tracking of its quarterly release data.  This project would seek to fully automate and consolidate the quantification of release data measurement for metrics such as the number of pathways, reactions, distinct proteins (with and without UniProt isoforms), complexes, small molecules, drugs/therapeutics, literature references, etc. for human (curated) and non-human (electronically inferred) species and stratified for normal and disease biology. a centralized dashboard would be useful by the team for discussing metrics externally and community outreach.  * ''Expected results:'' A program which will produce a standardized report of statistics for a Reactome release database with aesthetic visuals * ''Expected results:'' A program which will produce a standardized report of statistics for a Reactome release database with aesthetic visuals  * ''Project Home Page URL:'' [https://reactome.org. reactome.org]. * ''Project Home Page URL:'' [https://reactome.org. reactome.org].  * ''Knowledge prerequisites:'' Java, MySQL and/or Neo4j, creating visuals for statistical data (preferred but not required) * ''Knowledge prerequisites:'' Java, MySQL and/or Neo4j, creating visuals for statistical data (preferred but not required)  * ''Skill level:'' Medium. * ''Skill level:'' Medium. −* ''Mentors:'' Joel Weiser (joel.weiser[AT]oicr.on.ca)+* ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Joel Weiser (joel.weiser[AT]oicr.on.ca)     == Community data submission (WormBase) == == Community data submission (WormBase) == Robin.haw
Categories: Bio

GSOC Project Ideas 2020

Thu, 03/05/2020 - 14:25

‎Community data submission (WormBase)

← Older revision Revision as of 19:25, 5 March 2020 Line 105: Line 105:  * ''Knowledge prerequisites:'' JavaScript, experience building cloud native solution preferred. * ''Knowledge prerequisites:'' JavaScript, experience building cloud native solution preferred.  * ''Skill level:'' Advanced * ''Skill level:'' Advanced −* ''Mentors:'' Todd Harris (todd[AT]wormbase.org), Sibyl Gao (sibyl[AT]wormbase.org).+* ''Mentors:'' Todd Harris (todd[AT]wormbase.org), Sibyl Gao (sibyl[AT]wormbase.org), Juancarlos Chan (azurebrd[AT]its.caltech.edu).     == Data Table functionality and performance (WormBase) == == Data Table functionality and performance (WormBase) == Sibyl
Categories: Bio

GSOC Project Ideas 2020

Thu, 02/20/2020 - 18:41

← Older revision Revision as of 23:41, 20 February 2020 Line 153: Line 153:     == JBrowse 2 - Phylogenetic tree viewer == == JBrowse 2 - Phylogenetic tree viewer == −* ''Brief explanation:'' Write a new view plugin for the upcoming JBrowse 2 genome browser that shows phylogenetic trees, either in the traditional "tree" format, or in a nested collapsable list. Users can then select several species in the phylogeny and launch the existing JBrowse 2 comparative synteny view from them.+* ''Brief explanation:'' Comparative genomic data is arriving faster than ever, and building phylogenetic views directly into the user interface will be critical for evolutionary biologists to understand and interpret this data. This project will involve writing a new view for the upcoming JBrowse 2 genome browser that shows phylogenetic trees, either in the traditional "tree" format, or in a nested collapsable list. Users can then select several species in the phylogeny and launch the existing JBrowse 2 comparative synteny view from them.  * ''Expected results:'' A beautiful and fast tree viewer in JBrowse 2, written using React and mobx-state-tree. * ''Expected results:'' A beautiful and fast tree viewer in JBrowse 2, written using React and mobx-state-tree.  * ''Project Home Page URL:'' https://jbrowse.org   * ''Project Home Page URL:'' https://jbrowse.org   Line 160: Line 160:  * ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie) * ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie)    −== JBrowse 2 - Genomic Variant Effect Visualization ==+== JBrowse 2 - Ensembl VEP integration == −* ''Brief explanation:'' Add features to JBrowse 2 that allow visualizing the predicted phenotypic impact of variants. Add an integration with the Ensembl Variant Effect Predictor (VEP) to query and show predicted variant effects.+* ''Brief explanation:'' Predicting the impact - deleterious or neutral - of a genomic variant is an important task for clinical genomics. This project will add features to JBrowse 2 that allow visualizing the predicted phenotypic impact of variants. It will use integration with the Ensembl Variant Effect Predictor (VEP) via REST API to query and show predicted variant effects.  * ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects * ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects  * ''Project Home Page URL:'' https://jbrowse.org   * ''Project Home Page URL:'' https://jbrowse.org   Line 169: Line 169:     == JBrowse 2 - Genomic Variant Evidence Visualization == == JBrowse 2 - Genomic Variant Evidence Visualization == −* ''Brief explanation:'' Add features to JBrowse 2 that improve the visualization of the supporting evidence for a specific genome variant. This could include highlighting sequencing reads that seem to be consistent with the presence of a variant, providing a pop-up "report" about supporting evidence, or other.  +* ''Brief explanation:'' Drilling into the evidence for an individual variant will be a routine task in personalized genomic medicine. This project will add features to JBrowse 2 that improve the visualization of the supporting evidence for a specific variant. This could include highlighting sequencing reads that seem to be consistent with the presence of a variant, providing a pop-up "report" about supporting evidence, or other.    * ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects * ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects  * ''Project Home Page URL:'' https://jbrowse.org   * ''Project Home Page URL:'' https://jbrowse.org   Colin Diesh
Categories: Bio

2011 GMOD Spring Training

Tue, 02/11/2020 - 18:28

‎Schedule: type fix

← Older revision Revision as of 23:28, 11 February 2020 Line 67: Line 67:  <div style="font-weight: normal">A week long hands-on course on GMOD Component installation, configuration, and usage.  The course will cover these components in detail: <div style="font-weight: normal">A week long hands-on course on GMOD Component installation, configuration, and usage.  The course will cover these components in detail:    −'''[[Apollo]] &bull; [[MAKER]] &bull; [[GBrowse]] &bull; [[Chado]] &bull; [[InterMine]] &bull; [[JBrowse]] &bull; [[GBrowse_syn]] &bull; [[Tripal]] &bull; [[GFF3]] &bull; [[Galaxy]] &bull [[SOBA]]'''+'''[[Apollo]] &bull; [[MAKER]] &bull; [[GBrowse]] &bull; [[Chado]] &bull; [[InterMine]] &bull; [[JBrowse]] &bull; [[GBrowse_syn]] &bull; [[Tripal]] &bull; [[GFF3]] &bull; [[Galaxy]] &bull; [[SOBA]]'''  </div> </div>  |} |} Clements
Categories: Bio

Calendar

Tue, 02/11/2020 - 18:09

‎Other Calendars: Updated Galaxy events page link

← Older revision Revision as of 23:09, 11 February 2020 (One intermediate revision by the same user not shown)Line 20: Line 20:  * [https://www.google.com/calendar/feeds/mq93blfvdoosh5unpmivu4kh1c%40group.calendar.google.com/public/basic Galaxy Calendar] [[File:RSSIcon16x16.gif|Galaxy Calendar Feed]] * [https://www.google.com/calendar/feeds/mq93blfvdoosh5unpmivu4kh1c%40group.calendar.google.com/public/basic Galaxy Calendar] [[File:RSSIcon16x16.gif|Galaxy Calendar Feed]]    −  −==iAnn (Bioinformatics Events) Calendar==  −  −[http://iann.pro iAnn] lists events relevant to the broader scientific community.  −  −<iannwidget />        Line 32: Line 26:  {| {|  | | −* [http://wiki.galaxyproject.org/Events Galaxy events list]+* [http://galaxyproject.org/events Galaxy events list]  * [http://bioinformatics.oupjournals.org/cgi/calendarcontent Bioinformatics (journal) calender] * [http://bioinformatics.oupjournals.org/cgi/calendarcontent Bioinformatics (journal) calender]  * [http://www.embnet.org/event/all/list EMBnet events list] * [http://www.embnet.org/event/all/list EMBnet events list] Line 47: Line 41:  {{GMODEventsList}} {{GMODEventsList}}    −[[Category:GMOD Project]]+[[Category:GMOD_Project]] −[[Category:GMOD Community]]+[[Category:GMOD_Community]]  [[Category:Events]] [[Category:Events]] Clements
Categories: Bio

GSOC Project Ideas 2020

Thu, 02/06/2020 - 15:06

← Older revision Revision as of 20:06, 6 February 2020 (2 intermediate revisions by the same user not shown)Line 151: Line 151:  * ''Skill level:'' Advanced * ''Skill level:'' Advanced  * ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org). * ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org).  +  +== JBrowse 2 - Phylogenetic tree viewer ==  +* ''Brief explanation:'' Write a new view plugin for the upcoming JBrowse 2 genome browser that shows phylogenetic trees, either in the traditional "tree" format, or in a nested collapsable list. Users can then select several species in the phylogeny and launch the existing JBrowse 2 comparative synteny view from them.  +* ''Expected results:'' A beautiful and fast tree viewer in JBrowse 2, written using React and mobx-state-tree.  +* ''Project Home Page URL:'' https://jbrowse.org  +* ''Knowledge prerequisites:'' JavaScript, React  +* ''Skill level:'' Advanced  +* ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie)  +  +== JBrowse 2 - Genomic Variant Effect Visualization ==  +* ''Brief explanation:'' Add features to JBrowse 2 that allow visualizing the predicted phenotypic impact of variants. Add an integration with the Ensembl Variant Effect Predictor (VEP) to query and show predicted variant effects.  +* ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects  +* ''Project Home Page URL:'' https://jbrowse.org  +* ''Knowledge prerequisites:'' JavaScript, React  +* ''Skill level:'' Medium  +* ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie)  +  +== JBrowse 2 - Genomic Variant Evidence Visualization ==  +* ''Brief explanation:'' Add features to JBrowse 2 that improve the visualization of the supporting evidence for a specific genome variant. This could include highlighting sequencing reads that seem to be consistent with the presence of a variant, providing a pop-up "report" about supporting evidence, or other.  +* ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects  +* ''Project Home Page URL:'' https://jbrowse.org  +* ''Knowledge prerequisites:'' JavaScript, React  +* ''Skill level:'' Advanced  +* ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie) RobertBuels
Categories: Bio

GSOC Project Ideas 2020

Thu, 02/06/2020 - 15:04

← Older revision Revision as of 20:04, 6 February 2020 (One intermediate revision by the same user not shown)Line 151: Line 151:  * ''Skill level:'' Advanced * ''Skill level:'' Advanced  * ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org). * ''Mentors:'' Sibyl Gao (sibyl[AT]wormbase.org).  +  +== JBrowse 2 - Phylogenetic tree viewer ==  +* ''Brief explanation:'' Write a new view plugin for the upcoming JBrowse 2 genome browser that shows phylogenetic trees, either in the traditional "tree" format, or in a nested collapsable list. Users can then select several species in the phylogeny and launch the existing JBrowse 2 comparative synteny view from them.  +* ''Expected results:'' A beautiful and fast tree viewer in JBrowse 2, written using React and mobx-state-tree.  +* ''Project Home Page URL:'' https://jbrowse.org  +* ''Knowledge prerequisites:'' JavaScript, React  +* ''Skill level:'' Advanced  +* ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie)  +  +== JBrowse 2 - Genome Variant Effect Visualization ==  +* ''Brief explanation:'' Add features to JBrowse 2 that allow visualizing the predicted phenotypic impact of variants. Add an integration with the Ensembl Variant Effect Predictor (VEP) to query and show predicted variant effects.  +* ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects  +* ''Project Home Page URL:'' https://jbrowse.org  +* ''Knowledge prerequisites:'' JavaScript, React  +* ''Skill level:'' Medium  +* ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie)  +  +== JBrowse 2 - Genome Variant Evidence Visualization ==  +* ''Brief explanation:'' Add features to JBrowse 2 that improve the visualization of the supporting evidence for a specific genome variant. This could include highlighting sequencing reads that seem to be consistent with the presence of a variant, providing a pop-up "report" about supporting evidence, or other.  +* ''Expected results:'' New features in JBrowse 2 for predicting and visualizing variant effects  +* ''Project Home Page URL:'' https://jbrowse.org  +* ''Knowledge prerequisites:'' JavaScript, React  +* ''Skill level:'' Advanced  +* ''Mentors:'' JBrowse Development Team (Robert Buels, Colin Diesh, Garrett Stevens, or Peter Xie) RobertBuels
Categories: Bio

GSOC Project Ideas 2020

Thu, 02/06/2020 - 12:10

‎Create a software package for use in R to query Reactome’s Graph Database in Neo4J (Reactome)

← Older revision Revision as of 17:10, 6 February 2020 (10 intermediate revisions by the same user not shown)Line 52: Line 52:  **''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) and Joel Weiser (joel.weiser[AT]oicr.on.ca). **''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) and Joel Weiser (joel.weiser[AT]oicr.on.ca).    −== Create a software package for use in R to query Reactome’s Graph Database in Neo4J ==+== Create a software package for use in R to query Reactome’s Graph Database in Neo4J (Reactome) ==     *'''Project Idea Name (Project Name/Lab Name)''' *'''Project Idea Name (Project Name/Lab Name)''' Line 60: Line 60:  **''Knowledge prerequisites:''  R Programming Language, Neo4J. **''Knowledge prerequisites:''  R Programming Language, Neo4J.  **''Skill level:'' Medium. **''Skill level:'' Medium. −**''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca).+**''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca) and Guilherme Viteri (gviteri[AT]ebi.ac.uk).    − +== Automating Reactome’s data release post-step QA (Reactome) == −== Automating Reactome’s data release post-step QA ==+  * ''Brief explanation:'' * ''Brief explanation:''  ** Reactome is a free, open-source, curated and peer-reviewed pathway database. Every quarter we complete a data release that contains newly curated information as well as updated data from a variety of resources. Running the data release is time-intensive, in part due to the number of steps involved that require manual inspection to verify it was run correctly. ** Reactome is a free, open-source, curated and peer-reviewed pathway database. Every quarter we complete a data release that contains newly curated information as well as updated data from a variety of resources. Running the data release is time-intensive, in part due to the number of steps involved that require manual inspection to verify it was run correctly. Line 74: Line 73:  * ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca) * ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca)    −== GraphDB API for Reactome ==+== GraphDB API (Reactome) ==  * ''Brief explanation:'' Reactome uses both a relational database (MySQL) and a graph database (Neo4j). There is an existing API that uses the relational database, and many Reactome components use this API. To make it easier to transition these components to using the graph database, a new API with equivalent functionality needs to be created.   * ''Brief explanation:'' Reactome uses both a relational database (MySQL) and a graph database (Neo4j). There is an existing API that uses the relational database, and many Reactome components use this API. To make it easier to transition these components to using the graph database, a new API with equivalent functionality needs to be created.    * ''Expected results:'' A new Java API that interacts with the graph database, with functionality such that it could be used as a drop-in replacement for the relational database API. * ''Expected results:'' A new Java API that interacts with the graph database, with functionality such that it could be used as a drop-in replacement for the relational database API. Line 81: Line 80:  * ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary. * ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary.  * ''Skill level:'' Advanced. * ''Skill level:'' Advanced. −* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca),+* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca).  +   +== GraphQL interface for querying Reactome data (Reactome) ==  +* ''Brief explanation:'' Reactome currently has a REST-based API that allows end-users to obtain specific data from pre-defined queries.  To allow users to customize their queries, explore the Reactome data schema and better understand what data they can obtain, a GraphQL based endpoint could be added to the existing API.  +* ''Expected results:'' A publicly accessible GraphQL API that allows Reactome end-users to submit custom data queries to Reactome  +* ''Project Home Page URL:'' [https://reactome.org. reactome.org].  +* ''Knowledge prerequisites: Java, GraphQL, Neo4j (preferred), Swagger (optional)''  +* ''Skill level:'' Advanced.  +* ''Mentors:'' Joel Weiser (joel.weiser[AT]oicr.on.ca)  +   +== Statistics consolidation/display of release data (Reactome) ==  +* ''Brief explanation:'' Reactome has both manual and automated statistical tracking of its quarterly release data.  This project would seek to fully automate and consolidate the quantification of release data measurement for metrics such as the number of pathways, reactions, distinct proteins (with and without UniProt isoforms), complexes, small molecules, drugs/therapeutics, literature references, etc. for human (curated) and non-human (electronically inferred) species and stratified for normal and disease biology  +* ''Expected results:'' A program which will produce a standardized report of statistics for a Reactome release database with aesthetic visuals  +* ''Project Home Page URL:'' [https://reactome.org. reactome.org].  +* ''Knowledge prerequisites:'' Java, MySQL and/or Neo4j, creating visuals for statistical data (preferred but not required)  +* ''Skill level:'' Medium.  +* ''Mentors:'' Joel Weiser (joel.weiser[AT]oicr.on.ca)     == Community data submission (WormBase) == == Community data submission (WormBase) == Jweiser
Categories: Bio

GSOC Project Ideas 2020

Thu, 02/06/2020 - 10:48

‎Statistics consolidation and display of public release data (Reactome)

← Older revision Revision as of 15:48, 6 February 2020 (9 intermediate revisions by the same user not shown)Line 52: Line 52:  **''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) and Joel Weiser (joel.weiser[AT]oicr.on.ca). **''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) and Joel Weiser (joel.weiser[AT]oicr.on.ca).    −== Create a software package for use in R to query Reactome’s Graph Database in Neo4J ==+== Create a software package for use in R to query Reactome’s Graph Database in Neo4J (Reactome) ==     *'''Project Idea Name (Project Name/Lab Name)''' *'''Project Idea Name (Project Name/Lab Name)''' Line 62: Line 62:  **''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca). **''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca).    − +== Automating Reactome’s data release post-step QA (Reactome) == −== Automating Reactome’s data release post-step QA ==+  * ''Brief explanation:'' * ''Brief explanation:''  ** Reactome is a free, open-source, curated and peer-reviewed pathway database. Every quarter we complete a data release that contains newly curated information as well as updated data from a variety of resources. Running the data release is time-intensive, in part due to the number of steps involved that require manual inspection to verify it was run correctly. ** Reactome is a free, open-source, curated and peer-reviewed pathway database. Every quarter we complete a data release that contains newly curated information as well as updated data from a variety of resources. Running the data release is time-intensive, in part due to the number of steps involved that require manual inspection to verify it was run correctly. Line 74: Line 73:  * ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca) * ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca)    −== GraphDB API for Reactome ==+== GraphDB API (Reactome) ==  * ''Brief explanation:'' Reactome uses both a relational database (MySQL) and a graph database (Neo4j). There is an existing API that uses the relational database, and many Reactome components use this API. To make it easier to transition these components to using the graph database, a new API with equivalent functionality needs to be created.   * ''Brief explanation:'' Reactome uses both a relational database (MySQL) and a graph database (Neo4j). There is an existing API that uses the relational database, and many Reactome components use this API. To make it easier to transition these components to using the graph database, a new API with equivalent functionality needs to be created.    * ''Expected results:'' A new Java API that interacts with the graph database, with functionality such that it could be used as a drop-in replacement for the relational database API. * ''Expected results:'' A new Java API that interacts with the graph database, with functionality such that it could be used as a drop-in replacement for the relational database API. Line 81: Line 80:  * ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary. * ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary.  * ''Skill level:'' Advanced. * ''Skill level:'' Advanced. −* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca),+* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca).  +   +== GraphQL interface for querying Reactome data (Reactome) ==  +* ''Brief explanation:'' Reactome currently has a REST-based API that allows end-users to obtain specific data from pre-defined queries.  To allow users to customize their queries, explore the Reactome data schema and better understand what data they can obtain, a GraphQL based endpoint could be added to the existing API.  +* ''Expected results:'' A publicly accessible GraphQL API that allows Reactome end-users to submit custom data queries to Reactome  +* ''Project Home Page URL:'' [https://reactome.org. reactome.org].  +* ''Knowledge prerequisites: Java, GraphQL, Neo4j (preferred), Swagger (optional)''  +* ''Skill level:'' Advanced.  +* ''Mentors:'' Joel Weiser (joel.weiser[AT]oicr.on.ca)  +   +== Statistics consolidation/display of release data (Reactome) ==  +* ''Brief explanation:'' Reactome has both manual and automated statistical tracking of its quarterly release data.  This project would seek to fully automate and consolidate the quantification of release data measurement for metrics such as the number of pathways, reactions, distinct proteins (with and without UniProt isoforms), complexes, small molecules, drugs/therapeutics, literature references, etc. for human (curated) and non-human (electronically inferred) species and stratified for normal and disease biology  +* ''Expected results:'' A program which will produce a standardized report of statistics for a Reactome release database with aesthetic visuals  +* ''Project Home Page URL:'' [https://reactome.org. reactome.org].  +* ''Knowledge prerequisites:'' Java, MySQL and/or Neo4j, creating visuals for statistical data (preferred but not required)  +* ''Skill level:'' Medium.  +* ''Mentors:'' Joel Weiser (joel.weiser[AT]oicr.on.ca)     == Community data submission (WormBase) == == Community data submission (WormBase) == Jweiser
Categories: Bio

GSOC Project Ideas 2020

Wed, 02/05/2020 - 15:41

‎GraphDB API for Reactome

← Older revision Revision as of 20:41, 5 February 2020 (2 intermediate revisions by the same user not shown)Line 61: Line 61:  **''Skill level:'' Medium. **''Skill level:'' Medium.  **''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca). **''Mentors:''  Joel Weiser (joel.weiser[AT]oicr.on.ca).  +  +  +== Automating Reactome’s data release post-step QA ==  +* ''Brief explanation:''  +** Reactome is a free, open-source, curated and peer-reviewed pathway database. Every quarter we complete a data release that contains newly curated information as well as updated data from a variety of resources. Running the data release is time-intensive, in part due to the number of steps involved that require manual inspection to verify it was run correctly.  +** The project will involve the developer building QA steps that can automatically verify the data release steps ran correctly. The data release can be divided into MySQL or Neo4j components, and the student can choose to work on QA for either or both.  +* ''Expected results:'' QA code that automatically verifies release steps were correctly run. The new QA tests will encompass data checks within the MySQL and/or Neo4j databases as well as comparisons between data releases.  +* ''Project Home Page URL:'' https://reactome.org/  +* ''Project paper reference and URL:''  +* ''Knowledge prerequisites:''  Java, MySQL, (optional) Neo4j, AWS  +* ''Skill level:'' Medium  +* ''Mentors:'' Justin Cook (justin.cook[AT]oicr.on.ca)  +  +== GraphDB API for Reactome ==  +* ''Brief explanation:'' Reactome uses both a relational database (MySQL) and a graph database (Neo4j). There is an existing API that uses the relational database, and many Reactome components use this API. To make it easier to transition these components to using the graph database, a new API with equivalent functionality needs to be created.  +* ''Expected results:'' A new Java API that interacts with the graph database, with functionality such that it could be used as a drop-in replacement for the relational database API.  +* ''Project Home Page URL:'' [https://reactome.org/ reactome.org].  +* ''Project paper reference and URL:''  +* ''Knowledge prerequisites:''  Java, MySQL. Neo4j would be good, but not necessary.  +* ''Skill level:'' Advanced.  +* ''Mentors:'' Solomon Shorser (solomon.shorser[AT]oicr.on.ca),     == Community data submission (WormBase) == == Community data submission (WormBase) == Sshorser
Categories: Bio

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